rs203462
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007202.4(AKAP10):āc.1936A>Gā(p.Ile646Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 1,612,096 control chromosomes in the GnomAD database, including 125,833 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_007202.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP10 | NM_007202.4 | c.1936A>G | p.Ile646Val | missense_variant | 14/15 | ENST00000225737.11 | |
AKAP10 | NM_001330152.2 | c.1762A>G | p.Ile588Val | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP10 | ENST00000225737.11 | c.1936A>G | p.Ile646Val | missense_variant | 14/15 | 1 | NM_007202.4 | P1 | |
AKAP10 | ENST00000395536.7 | c.1762A>G | p.Ile588Val | missense_variant | 13/14 | 5 | |||
AKAP10 | ENST00000578898.1 | c.*269A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 3 | ||||
AKAP10 | ENST00000583951.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.427 AC: 64970AN: 151984Hom.: 14728 Cov.: 33
GnomAD3 exomes AF: 0.371 AC: 93016AN: 250460Hom.: 18352 AF XY: 0.364 AC XY: 49250AN XY: 135416
GnomAD4 exome AF: 0.385 AC: 562722AN: 1459994Hom.: 111071 Cov.: 37 AF XY: 0.382 AC XY: 277236AN XY: 726326
GnomAD4 genome ? AF: 0.428 AC: 65059AN: 152102Hom.: 14762 Cov.: 33 AF XY: 0.424 AC XY: 31542AN XY: 74368
ClinVar
Submissions by phenotype
Cardiac conduction defect, susceptibility to Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | May 15, 2007 | - - |
AKAP10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at